Updating molecule causes hang when saving

Hi there,

We just implimented Marvin Sketch Applet 6.2 on our chemical data production site.  We run our site in Tomcat- with a great deal of memory assigned to it. We update the Chemaxon structure table within our website so we can perform other operations before and after the save. 

This has been working well, but when a user has tried to enter a particular diagram drawn in Marvin sketch we find that on  UpdateHandler.execute(true), it hangs using more and more memory from tomcat until the entire site is brought down! 

We get the following message in the log:

Accepted unusual valence(s): O(3); O(6); Metal was disconnected

As you can understand this is an urgent issue.  Below is the code I am using for the updating the structure and I have attached the marvin file of the problem compound.

      
        ConnectionHandler conh = new ConnectionHandler(connection, ConnectionHandler.DEFAULT_PROPERTY_TABLE);
        PreparedStatement tStatement = null;
        UpdateHandler uh = null;
 
        try {

            connection.setAutoCommit(false); //transaction block start
            String structureTableName = "PROD.CHEMAXON_STRUCTURES";
            uh = new UpdateHandler(conh, UpdateHandler.UPDATE, structureTableName, "INCHI, INCHI_KEY");            
            uh.setStructure(dto.getCdStructure());
         Long tempId = dto.getCdId();
            uh.setID(tempId.intValue());
           
            uh.setDuplicateFiltering(UpdateHandler.DUPLICATE_FILTERING_OFF);
         
            cd_id = uh.execute(true);

......

 Many thanks

Megan

Hi Megan,

I don't know what is going on there. I can't import the molecule in InstantJChem. I can open it in MarvinSketch, but when hitting "Add" button the following stacktrace occur:

java.lang.OutOfMemoryError: Java heap space

	at java.util.Arrays.copyOf(Arrays.java:2734)

	at java.util.ArrayList.ensureCapacity(ArrayList.java:167)

	at java.util.ArrayList.add(ArrayList.java:351)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:669)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

	at chemaxon.core.calculations.stereo.AXCTStereoDetection.findActiveAtomPairs(AXCTStereoDetection.java:674)

Hi Megan,

We've managed to reproduce the issue. Unfortunately it looks like there is no workaround for it.

We will fix it as soon as possible.

Thank you for the report.

Regards,

Peter

Hi Megan,

We've managed to fix the bug, it will be released in the next patch release, 6.2.1.

Regards,

Peter

That is great- when can we get the patch?  We are quite anxious to get a hold of it!

Thanks

Megan

Hi there,

I was wondering when the patch for 6.2.1 will be available?  This is creating some major issues for us as it is bringing down our tomcat server!

Thanks very much

Megan

Hi Megan,

I did let know our release coordinator that the 6.2.1 release is very urgent for you. He said that it is possible that we will have it this week,  and it is most likely that we will have it next week.

I hope that this is acceptable for you.

Best regards,

Zsuzsa

thanks very much,  I will look out for it.

Thanks very much

Megan

Hi Megan,

I'm happy to inform you that version 6.2.1 is out.

You can download it from: http://www.chemaxon.com/download/

Regards,

Peter

Just update to Marvin 6.2.1 and it has fixed the problem.  Thanks very much!

Regards

Megan